Biochemistry, sometimes called biological chemistry, is the study of chemical

processes within, and relating to, living organisms.[1] By controlling information

flow through biochemical signaling and the flow of chemical energy through
metabolism, biochemical processes cause the complexity of life. Over the last 40
years, biochemistry has become so successful at explaining living processes that
now almost all areas of the life sciences from botany to medicine are engaged in
biochemical research.[2] Today, the main focus of pure biochemistry is in
understanding how biological molecules give rise to the processes that occur
within living cells, which in turn relates greatly to the study and understanding of
whole organisms.
Biochemistry is closely related to molecular biology, the study of the molecular
mechanisms by which genetic information encoded in DNA is able to result in the
processes of life. Depending on the exact definition of the terms used, molecular
biology can be thought of as a branch of biochemistry, or biochemistry as a tool
with which to investigate and study molecular biology.
Much of biochemistry deals with the structures, functions and interactions of
biological macromolecules, such as proteins, nucleic acids, carbohydrates and
lipids, which provide the structure of cells and perform many of the functions
associated with life. The chemistry of the cell also depends on the reactions of
smaller molecules and ions. These can be inorganic, for example water and metal
ions, or organic, for example the amino acids which are used to synthesize
proteins. The mechanisms by which cells harness energy from their environment
via chemical reactions are known as metabolism. The findings of biochemistry are
applied primarily in medicine, nutrients, and agriculture. in nutrients, biochemist,
investigate the causes and cures of disease.in nutrients, they study how to maintain
health and study the effects of nutritional deficiencies. In agriculture, biochemists
investigate soil and fertilizers, and try to discover ways to improve crop
cultivation, crop storage and pest control.

History
It once was generally believed that life and its materials had some essential
property or substance distinct from any found in non-living matter, and it was
thought that only living beings could produce the molecules of life Then, in 1828,
Friedrich Wohler published a paper on the synthesis of urea, proving that organic
compounds can be created artificially.[3]

The dawn of biochemistry may have been the discovery of the first enzyme,
diastase (today called amylase), in 1833 by Anselme Payen.[4] Eduard Buchner
contributed the first demonstration of a complex biochemical process outside a cell
in 1896: alcoholic fermentation in cell extracts of yeast.[5] Although the term
"biochemistry" seems to have been first used in 1882, it is generally accepted that
the formal coinage of biochemistry occurred in 1903 by Carl Neuberg, a German
chemist.[6] Since then, biochemistry has advanced, especially since the mid-20th
century, with the development of new techniques such as chromatography, X-ray
diffraction, dual polarisation interferometry, NMR spectroscopy, radioisotopic
labeling, electron microscopy, and molecular dynamics simulations. These
techniques allowed for the discovery and detailed analysis of many molecules and
metabolic pathways of the cell, such as glycolysis and the Krebs cycle (citric acid
cycle).
Another significant historic event in biochemistry is the discovery of the gene and
its role in the transfer of information in the cell. This part of biochemistry is often
called molecular biology.[7] In the 1950s, James D. Watson, Francis Crick, Rosalind
Franklin, and Maurice Wilkins were instrumental in solving DNA structure and
suggesting its relationship with genetic transfer of information.[8] In 1958, George
Beadle and Edward Tatum received the Nobel Prize for work in fungi showing that
one gene produces one enzyme.[9] In 1988, Colin Pitchfork was the first person
convicted of murder with DNA evidence, which led to growth of forensic science.
[10]
More recently, Andrew Z. Fire and Craig C. Mello received the 2006 Nobel
Prize for discovering the role of RNA interference (RNAi), in the silencing of gene
expression.[11]
Starting materials: the chemical elements of life
Main articles: Composition of the human body and Dietary mineral
Around two dozen of the 92 naturally occurring chemical elements are essential to
various kinds of biological life. Most rare elements on Earth is not needed by life
(exceptions being selenium and iodine), while a few common ones (aluminum and
titanium) are not used. Most organisms share element needs, but there are a few
differences between plants and animals. For example ocean algae use bromine but
land plants and animals seem to need none. All animals require sodium, but some
plants do not. Plants need boron and silicon, but animals may not (or may need
ultra-small amounts).

Just six elementscarbon, hydrogen, nitrogen, oxygen, calcium, and phosphorus

make up almost 99% of the mass of a human body (see composition of the
human body for a complete list). In addition to the six major elements that
compose most of the human body, humans require smaller amounts of possibly 18
more.[12]
Biomolecules
The four main classes of molecules in biochemistry are carbohydrates, lipids,
proteins, and nucleic acids. Many biological molecules are polymers: in this
terminology, monomers are relatively small micro molecules that are linked
together to create large macromolecules, which are known as polymers. When
monomers are linked together to synthesize a biological polymer, they undergo a
process called dehydration synthesis. Different macromolecules can assemble in
larger complexes, often needed for biological activity.

Carbohydrates

A molecule of sucrose (glucose + fructose), a disaccharide.

Carbohydrates are made from monomers called monosaccharides. Some of these
monosaccharides include glucose (C6H12O6), fructose (C6H12O6), and deoxyribose
(C5H10O4). When two monosaccharides undergo dehydration synthesis, water is
produced, as two hydrogen atoms and one oxygen atom are lost from the two
monosaccharides' hydroxyl group.

Lipids
Main articles: Lipid, Glycerol, and Fatty acid

A triglyceride with a glycerol molecule on the left and three fatty acids coming off
it.
Lipids are usually made from one molecule of glycerol combined with other
molecules. In triglycerides, the main group of bulk lipids, there is one molecule of
glycerol and three fatty acids. Fatty acids are considered the monomer in that case,
and may be saturated (no double bonds in the carbon chain) or unsaturated (one or
more double bonds in the carbon chain).
Lipids, especially phospholipids, are also used in various pharmaceutical products,
either as co-solubilisers (e.g., in parenteral infusions) or else as drug carrier
components (e.g., in a liposome or transfersome).

Proteins

The general structure of an -amino acid, with the amino group on the left and the
carboxyl group on the right.
Proteins are very large molecules macro-biopolymers made from monomers
called amino acids. There are 20 standard amino acids, each containing a carboxyl
group, an amino group, and a side-chain (known as an "R" group). The "R" group
is what makes each amino acid different, and the properties of the side-chains
greatly influence the overall three-dimensional conformation of a protein. When
amino acids combine, they form a special bond called a peptide bond through
dehydration synthesis, and become a polypeptide, or protein.
In order to determine whether two proteins are related, or in other words to decide
whether they are homologous or not, scientists use sequence-comparison methods.
Methods like Sequence Alignments and Structural Alignments are powerful tools
that help scientists identify homologies between related molecules.[13]
The relevance of finding homologies among proteins goes beyond forming an
evolutionary pattern of protein families. By finding how similar two protein
sequences are, we acquire knowledge about their structure and therefore their
function.

Nucleic acids

The structure of deoxyribonucleic acid (DNA), the picture shows the monomers
being put together.
Nucleic acids are the molecules that make up DNA, an extremely important
substance that all cellular organisms use to store their genetic information. The
most common nucleic acids are deoxyribonucleic acid and ribonucleic acid. Their
monomers are called nucleotides. The most common nucleotides are adenine,
cytosine, guanine, thymine, and uracil. Adenine binds with thymine and uracil;
Thymine binds only with adenine; and cytosine and guanine can bind only with
one another.

Carbohydrates

The function of carbohydrates includes energy storage and providing structure.

Sugars are carbohydrates, but not all carbohydrates are sugars. There are more
carbohydrates on Earth than any other known type of biomolecule; they are used to
store energy and genetic information, as well as play important roles in cell to cell
interactions and communications.

Monosaccharides

Glucose
The simplest type of carbohydrate is a monosaccharide, which between other
properties contains carbon, hydrogen, and oxygen, mostly in a ratio of 1:2:1
(generalized formula CnH2nOn, where n is at least 3). Glucose, one of the most
important carbohydrates, is an example of a monosaccharide. So is fructose, the
sugar commonly associated with the sweet taste of fruits.[14][a] Some carbohydrates
(especially after condensation to oligo- and polysaccharides) contain less carbon
relative to H and O, which still are present in 2:1 (H:O) ratio. Monosaccharides can
be grouped into aldoses (having an aldehyde group at the end of the chain, e.g.
glucose) and ketoses (having a keto group in their chain; e.g. fructose). Both
aldoses and ketoses occur in an equilibrium (starting with chain lengths of C4)
cyclic forms. These are generated by bond formation between one of the hydroxyl
groups of the sugar chain with the carbon of the aldehyde or keto group to form a
hemiacetal bond. This leads to saturated five-membered (in furanoses) or sixmembered (in pyranoses) heterocyclic rings containing one O as heteroatom.

Disaccharides
Sucrose: ordinary table sugar and probably the most familiar carbohydrate.
Two monosaccharides can be joined using dehydration synthesis, in which a
hydrogen atom is removed from the end of one molecule and a hydroxyl group (
OH) is removed from the other; the remaining residues are then attached at the
sites from which the atoms were removed. The HOH or H2O is then released as
a molecule of water, hence the term dehydration. The new molecule, consisting of
two monosaccharides, is called a disaccharide and is conjoined together by a
glycosidic or ether bond. The reverse reaction can also occur, using a molecule of
water to split up a disaccharide and break the glycosidic bond; this is termed
hydrolysis. The most well-known disaccharide is sucrose, ordinary sugar (in
scientific contexts, called table sugar or cane sugar to differentiate it from other
sugars). Sucrose consists of a glucose molecule and a fructose molecule joined
together. Another important disaccharide is lactose, consisting of a glucose
molecule and a galactose molecule. As most humans age, the production of lactase,
the enzyme that hydrolyzes lactose back into glucose and galactose, typically
decreases. This results in lactase deficiency, also called lactose intolerance.
Sugar polymers are characterized by having reducing or non-reducing ends. A
reducing end of a carbohydrate is a carbon atom that can be in equilibrium with the
open-chain aldehyde or keto form. If the joining of monomers takes place at such a
carbon atom, the free hydroxyl group of the pyranose or furanose form is
exchanged with an OH-side-chain of another sugar, yielding a full acetal. This
prevents opening of the chain to the aldehyde or keto form and renders the
modified residue non-reducing. Lactose contains a reducing end at its glucose
moiety, whereas the galactose moiety form a full acetal with the C4-OH group of
glucose. Saccharose does not have a reducing end because of full acetal formation
between the aldehyde carbon of glucose (C1) and the keto carbon of fructose (C2).

Oligosaccharides and polysaccharides

Cellulose as polymer of -D-glucose
When a few (around three to six) monosaccharides are joined, it is called an
oligosaccharide (oligo- meaning "few"). These molecules tend to be used as
markers and signals, as well as having some other uses. Many monosaccharides
joined together make a polysaccharide. They can be joined together in one long
linear chain, or they may be branched. Two of the most common polysaccharides
are cellulose and glycogen, both consisting of repeating glucose monomers.
Cellulose is made by plants and is an important structural component of their
cell walls. Humans can neither manufacture nor digest it.
Glycogen, on the other hand, is an animal carbohydrate; humans and other
animals use it as a form of energy storage.
Use of carbohydrates as an energy source

Glucose is the major energy source in most life forms. For instance,
polysaccharides are broken down into their monomers (glycogen phosphorylase
removes glucose residues from glycogen). Disaccharides like lactose or sucrose are
cleaved into their two component monosaccharides.

Glycolysis (anaerobic)
Glucose is mainly metabolized by a very important ten-step pathway called
glycolysis, the net result of which is to break down one molecule of glucose into
two molecules of pyruvate; this also produces a net two molecules of ATP, the
energy currency of cells, along with two reducing equivalents as converting NAD+
to NADH. This does not require oxygen; if no oxygen is available (or the cell
cannot use oxygen), the NAD is restored by converting the pyruvate to lactate

(lactic acid) (e.g., in humans) or to ethanol plus carbon dioxide (e.g., in yeast).
Other monosaccharides like galactose and fructose can be converted into
intermediates of the glycolytic pathway.[15]

Aerobic
In aerobic cells with sufficient oxygen, as in most human cells, the pyruvate is
further metabolized. It is irreversibly converted to acetyl-CoA, giving off one
carbon atom as the waste product carbon dioxide, generating another reducing
equivalent as NADH. The two molecules acetyl-CoA (from one molecule of
glucose) then enter the citric acid cycle, producing two more molecules of ATP, six
more NADH molecules and two reduced (ubi)quinones (via FADH2 as enzymebound cofactor), and releasing the remaining carbon atoms as carbon dioxide. The
produced NADH and quinol molecules then feed into the enzyme complexes of the
respiratory chain, an electron transport system transferring the electrons ultimately
to oxygen and conserving the released energy in the form of a proton gradient over
a membrane (inner mitochondrial membrane in eukaryotes). Thus, oxygen is
reduced to water and the original electron acceptors NAD+ and quinone are
regenerated. This is why humans breathe in oxygen and breathe out carbon
dioxide. The energy released from transferring the electrons from high-energy
states in NADH and quinol is conserved first as proton gradient and converted to
ATP via ATP synthase. This generates an additional 28 molecules of ATP (24 from
the 8 NADH + 4 from the 2 quinols), totaling to 32 molecules of ATP conserved
per degraded glucose (two from glycolysis + two from the citrate cycle). It is clear
that using oxygen to completely oxidize glucose provides an organism with far
more energy than any oxygen-independent metabolic feature, and this is thought to
be the reason why complex life appeared only after Earth's atmosphere
accumulated large amounts of oxygen.

Gluconeogenesis

In vertebrates, vigorously contracting skeletal muscles (during weightlifting or

sprinting, for example) do not receive enough oxygen to meet the energy demand,
and so they shift to anaerobic metabolism, converting glucose to lactate. The liver
regenerates the glucose, using a process called gluconeogenesis. This process is not
quite the opposite of glycolysis, and actually requires three times the amount of
energy gained from glycolysis (six molecules of ATP are used, compared to the
two gained in glycolysis). Analogous to the above reactions, the glucose produced
can then undergo glycolysis in tissues that need energy, be stored as glycogen (or
starch in plants), or be converted to other monosaccharides or joined into di- or
oligosaccharides. The combined pathways of glycolysis during exercise, lactate's
crossing via the bloodstream to the liver, subsequent gluconeogenesis and release
of glucose into the bloodstream is called the Cori cycle.[16]

Proteins

A schematic of hemoglobin. The red and blue ribbons represent the protein globin;
the green structures are the heme groups.
Like carbohydrates, some proteins perform largely structural roles. For instance,
movements of the proteins actin and myosin ultimately are responsible for the

contraction of skeletal muscle. One property many proteins have is that they
specifically bind to a certain molecule or class of moleculesthey may be
extremely selective in what they bind. Antibodies are an example of proteins that
attach to one specific type of molecule. In fact, the enzyme-linked immunosorbent
assay (ELISA), which uses antibodies, is one of the most sensitive tests modern
medicine uses to detect various biomolecules. Probably the most important
proteins, however, are the enzymes. These molecules recognize specific reactant
molecules called substrates; they then catalyze the reaction between them. By
lowering the activation energy, the enzyme speeds up that reaction by a rate of 1011
or more: a reaction that would normally take over 3,000 years to complete
spontaneously might take less than a second with an enzyme. The enzyme itself is
not used up in the process, and is free to catalyze the same reaction with a new set
of substrates. Using various modifiers, the activity of the enzyme can be regulated,
enabling control of the biochemistry of the cell as a whole.
In essence, proteins are chains of amino acids. An amino acid consists of a carbon
atom bound to four groups. One is an amino group, NH2, and one is a carboxylic
acid group, COOH (although these exist as NH3+ and COO under
physiologic conditions). The third is a simple hydrogen atom. The fourth is
commonly denoted "R" and is different for each amino acid. There are 20
standard amino acids. Some of these have functions by themselves or in a modified
form; for instance, glutamate functions as an important neurotransmitter.

Generic amino acids (1) in neutral form, (2) as they exist physiologically, and (3)
joined together as a dipeptide.
Amino acids can be joined via a peptide bond. In this dehydration synthesis, a
water molecule is removed and the peptide bond connects the nitrogen of one
amino acid's amino group to the carbon of the other's carboxylic acid group. The
resulting molecule is called a dipeptide, and short stretches of amino acids (usually,
fewer than thirty) are called peptides or polypeptides. Longer stretches merit the
title proteins. As an example, the important blood serum protein albumin contains
585 amino acid residues.[17]

The structure of proteins is traditionally described in a hierarchy of four levels. The

primary structure of a protein simply consists of its linear sequence of amino acids;
for instance, "alanine-glycine-tryptophan-serine-glutamate-asparagine-glycinelysine-". Secondary structure is concerned with local morphology (morphology
being the study of structure). Some combinations of amino acids will tend to curl
up in a coil called an -helix or into a sheet called a -sheet; some -helixes can be
seen in the hemoglobin schematic above. Tertiary structure is the entire threedimensional shape of the protein. This shape is determined by the sequence of
amino acids. In fact, a single change can change the entire structure. The alpha
chain of hemoglobin contains 146 amino acid residues; substitution of the
glutamate residue at position 6 with a valine residue changes the behavior of
hemoglobin so much that it results in sickle-cell disease. Finally, quaternary
structure is concerned with the structure of a protein with multiple peptide
subunits, like hemoglobin with its four subunits. Not all proteins have more than
one subunit.[18]
Ingested proteins are usually broken up into single amino acids or dipeptides in the
small intestine, and then absorbed. They can then be joined to make new proteins.
Intermediate products of glycolysis, the citric acid cycle, and the pentose
phosphate pathway can be used to make all twenty amino acids, and most bacteria
and plants possess all the necessary enzymes to synthesize them. Humans and
other mammals, however, can synthesize only half of them. They cannot
synthesize isoleucine, leucine, lysine, methionine, phenylalanine, threonine,
tryptophan, and valine. These are the essential amino acids, since it is essential to
ingest them. Mammals do possess the enzymes to synthesize alanine, asparagine,
aspartate, cysteine, glutamate, glutamine, glycine, proline, serine, and tyrosine, the
nonessential amino acids. While they can synthesize arginine and histidine, they
cannot produce it in sufficient amounts for young, growing animals, and so these
are often considered essential amino acids.
If the amino group is removed from an amino acid, it leaves behind a carbon
skeleton called an -keto acid. Enzymes called transaminases can easily transfer
the amino group from one amino acid (making it an -keto acid) to another -keto
acid (making it an amino acid). This is important in the biosynthesis of amino
acids, as for many of the pathways, intermediates from other biochemical pathways
are converted to the -keto acid skeleton, and then an amino group is added, often
via transamination. The amino acids may then be linked together to make a protein.
[19]

A similar process is used to break down proteins. It is first hydrolyzed into its
component amino acids. Free ammonia (NH3), existing as the ammonium ion
(NH4+) in blood, is toxic to life forms. A suitable method for excreting it must
therefore exist. Different tactics have evolved in different animals, depending on
the animals' needs. Unicellular organisms, of course, simply release the ammonia
into the environment. Likewise, bony fish can release the ammonia into the water
where it is quickly diluted. In general, mammals convert the ammonia into urea,
via the urea cycle.[20]
Lipid
The term lipid composes a diverse range of molecules and to some extent is a
catchall for relatively water-insoluble or nonpolar compounds of biological origin,
including waxes, fatty acids, fatty-acid derived phospholipids, sphingolipids,
glycolipids, and terpenoids (e.g., retinoids and steroids). Some lipids are linear
aliphatic molecules, while others have ring structures. Some are aromatic, while
others are not. Some are flexible, while others are rigid.[21]
Most lipids have some polar character in addition to being largely nonpolar. In
general, the bulk of their structure is nonpolar or hydrophobic ("water-fearing"),
meaning that it does not interact well with polar solvents like water. Another part
of their structure is polar or hydrophilic ("water-loving") and will tend to associate
with polar solvents like water. This makes them amphiphilic molecules (having
both hydrophobic and hydrophilic portions). In the case of cholesterol, the polar
group is a mere -OH (hydroxyl or alcohol). In the case of phospholipids, the polar
groups are considerably larger and more polar, as described below.
Lipids are an integral part of our daily diet. Most oils and milk products that we
use for cooking and eating like butter, cheese, ghee etc., are composed of fats.
Vegetable oils are rich in various polyunsaturated fatty acids (PUFA). Lipidcontaining foods undergo digestion within the body and are broken into fatty acids
and glycerol, which are the final degradation products of fats and lipids.
Nucleic acids

A nucleic acid is a complex, high-molecular-weight biochemical macromolecule

composed of nucleotide chains that convey genetic information. The most common
nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA).
Nucleic acids are found in all living cells and viruses. Aside from the genetic

material of the cell, nucleic acids often play a role as second messengers, as well as
forming the base molecule for adenosine triphosphate, the primary energy-carrier
molecule found in all living organisms.
Nucleic acid, so called because of its prevalence in cellular nuclei, is the generic
name of the family of biopolymers. The monomers are called nucleotides, and each
consists of three components: a nitrogenous heterocyclic base (either a purine or a
pyrimidine), a pentose sugar, and a phosphate group. Different nucleic acid types
differ in the specific sugar found in their chain (e.g., DNA or deoxyribonucleic acid
contains 2-deoxyriboses). Also, the nitrogenous bases possible in the two nucleic
acids are different: adenine, cytosine, and guanine occur in both RNA and DNA,
while thymine occurs only in DNA and uracil occurs in RNA.[22]
Relationship to other "molecular-scale" biological sciences

Schematic relationship between biochemistry, genetics, and molecular biology

Researchers in biochemistry use specific techniques native to biochemistry, but
increasingly combine these with techniques and ideas developed in the fields of
genetics, molecular biology and biophysics. There has never been a hard-line
among these disciplines in terms of content and technique. Today, the terms
molecular biology and biochemistry are nearly interchangeable. The following
figure is a schematic that depicts one possible view of the relationship between the
fields:
Biochemistry is the study of the chemical substances and vital processes
occurring in living organisms. Biochemists focus heavily on the role,
function, and structure of biomolecules. The study of the chemistry behind

biological processes and the synthesis of biologically active molecules are

examples of biochemistry.
Genetics is the study of the effect of genetic differences on organisms. Often
this can be inferred by the absence of a normal component (e.g., one gene).
The study of "mutants" organisms with a changed gene that leads to the
organism being different with respect to the so-called "wild type" or normal
phenotype. Genetic interactions (epistasis) can often confound simple
interpretations of such "knock-out" or "knock-in" studies.
Molecular biology is the study of molecular underpinnings of the process of
replication, transcription and translation of the genetic material. The central
dogma of molecular biology where genetic material is transcribed into RNA
and then translated into protein, despite being an oversimplified picture of
molecular biology, still provides a good starting point for understanding the
field. This picture, however, is undergoing revision in light of emerging
novel roles for RNA.[23]
Chemical Biology seeks to develop new tools based on small molecules that
allow minimal perturbation of biological systems while providing detailed
information about their function. Further, chemical biology employs
biological systems to create non-natural hybrids between biomolecules and
synthetic devices (for example emptied